Photoswitchable Markers

Photoswitchable Markers for Optochemical Oligo Control

Reversible, light‑controlled moieties—azobenzene (incl. visible‑light variants), arylazopyrazole, diazocine, diarylethene, and spiropyran—to modulate hybridization, structure, and capture/release on demand.

Overview

Photoswitchable markers reversibly change conformation/absorption when illuminated, enabling optical control of hybridization, conformation, quenching, or capture. In oligonucleotides, azobenzene and related families can stabilize/destabilize duplexes in one state and reverse under another wavelength or via thermal relaxation—ideal for photo‑gated hybridization, switchable toeholds, aptamer capture/release, and molecular logic.

Azobenzene dT (Azo‑dT) o‑Fluoro Azo (visible) Arylazopyrazole Diazocine Diarylethene / Spiropyran
Why photoswitch?
  • Reversible ON/OFF control (no reagents)
  • Temporal/spatial precision via λ
  • Programmable kinetics & fatigue
Typical wavelengths
  • UV/violet ≈340–405 nm (trans→cis)
  • Blue/green ≈450–560 nm (cis→trans or vis variants)
  • Thermal relaxation: min→days
QC & docs
  • HPLC/UPLC; LC‑MS identity
  • Optional switching plots & fatigue cycles
  • RUO → GMP‑like documentation

Selection Guide

Family Switch Typical λ cis t1/2 Fatigue Notes Best‑fit uses Code
Azobenzene trans ⇄ cis 365 ↔ 450–520 nm / thermal min→h Good Robust; trans stacks, cis bends Photo‑gated hybridization; beacons [Azo‑dT]
o‑Fluoro Azo visible trans ⇄ cis 405–520 nm bidirectional h→days Very good Red‑shifted; long‑lived cis Visible‑only instruments [oF‑Azo]
Arylazopyrazole high‑contrast 365–405 ⇄ 520–560 nm hours→days Excellent Near‑quantitative switching Memory/logic designs [AZP‑Link]
Diazocine cis⇄trans 405–530 nm min→h Good Inverted stability Dark‑favored designs [Diazocine]
Diarylethene open ⇄ closed UV ⇄ visible stable Excellent Bistable; high fatigue resistance Binary memory; toggling [DTE‑Link]
Spiropyran SP ⇄ MC UV ⇄ visible sec→min Good Polarity/pH sensitive Sensing + switching [SP‑Link]
Hemithioindigo E ⇄ Z 450–560 nm min→h Good Visible‑only Vis‑only environments [HTI‑Link]
Tip: For visible‑only setups, prefer o‑fluoro azobenzene, AZP, diazocine, or HTI.

Chemistries & Placement

Azobenzene (Azo‑dT/internal)

Trans often stabilizes; cis bends/destabilizes. 1–3 units tune Tm shift.

Visible‑Light Azo (oF‑Azo)

Red‑shift into visible; improves biocompatibility and penetration.

Arylazopyrazole & Diazocine

High‑contrast (AZP) or inverted stability (diazocine) for extended states or dark‑favored designs.

Diarylethene (DTE)

Bistable open/closed; excellent fatigue—great for many cycles.

Spiropyran (SP)

SP↔MC switching couples optical contrast with environment sensitivity.

Attachment Geometry

Internal base replacements or pendant/backbone linkers; multiple units amplify effects.

Applications

Photo‑Gated Hybridization<

Toggle duplex formation or strand displacement with light.

Switchable Aptamer Capture/Release

Control binding and elution via light—no chaotropes or heat.

Molecular Logic & Memory

DTE/AZP support bistability and high cycle counts for logic/memory.

Products & Ordering

Product / Modification Description Function Application Code
Azobenzene‑dT (Azo‑dT) Internal base analog with reversible trans↔cis. Duplex modulation Hybridization gating; beacons; toeholds [Azo‑dT]
Visible‑Light Azobenzene (oF‑Azo) Ortho‑fluoro/push–pull variant operating in visible range. Vis‑range switching Live‑cell/tissue‑friendly [oF‑Azo]
Arylazopyrazole Linker High PSS contrast; long‑lived cis. Strong contrast Logic; long‑state storage [AZP‑Link]
Diazocine Linker Bridged azo with cis favored in dark. Dark‑state control Specialty gating [Diazocine]
Diarylethene (DTE) Linker Bistable open/closed; high fatigue resistance. Binary memory Robust repeated toggling [DTE‑Link]
Spiropyran (SP) Linker SP↔MC switch with environment sensitivity. Reporting + switching Sensing/control hybrids [SP‑Link]
Custom Photoswitch Oligo Sequence‑specific placement, purification, and validation. Turn‑key build Assay‑ready constructs [PS‑Custom]
Customizations: internal/pendant positions, multiple units, PEG/hexa‑EG spacers, mixed backbones (2′‑OMe/LNA), HPLC/UPLC, switching plots, and fatigue tests.

Technical Notes

  • Wavelength planning & filters. Match switch bands to LEDs/lasers and filters. For UV‑sensitive samples, use visible‑light azo, AZP, diazocine, or HTI.
  • Thermal relaxation & kinetics. cis→trans half‑life ranges minutes→days by scaffold/substituents; pick long‑lived for memory, short for rapid cycling.
  • Photofatigue & cycles. DTE and AZP offer strong fatigue resistance. Validate cycles under your irradiance and buffer conditions.
  • Placement rules. Internal base replacements maximize Tm modulation; multiple units amplify effect; avoid clustering in stable motifs unless intended.
  • Buffer compatibility. Avoid strong reducing agents that can reduce azo bonds; maintain oxygenated buffers for long irradiations.

Workflow

1
2
3
Design

Choose photoswitch family (Azo/AZP/DTE/SP/Diazocine/HTI), placement (internal/base vs linker), and wavelengths/filters.

Build

Synthesis with selected unit(s) → Purification (Desalt→HPLC/UPLC) → LC‑MS identity → Optional spectra & switching/fatigue tests.

Validate

Confirm λ/filters and cycle count; set visible/UV exposure as needed; finalize buffer and crosstalk/FRET checks.

Ready to spec your photoswitchable oligos?

Share sequence, wavelengths, placement, and cycle count—We’ll return a tuned design and QC plan.

Ordering Checklist

Sequence & placement
Target sequence and photoswitch position(s) (internal base vs linker; 5′/3′).
Family & wavelengths
Azo/AZP/DTE/SP/Diazocine/HTI and excitation/ emission or activation λ; filters/lasers available.
Cycle count & kinetics
Desired number of switching cycles; long‑lived vs fast‑relaxing needs.
Scale & purification
µmol → multi‑gram; Desalt vs HPLC/UPLC; spectral sheet/switching curves if needed.

FAQ

Photoswitchable vs. photocleavable—what’s the difference?

Photoswitchables are reversible (toggle between states). Photocleavables are irreversible (bond is broken).

Can I avoid UV altogether?

Yes—use visible‑light azobenzenes (e.g., o‑fluoro), arylazopyrazoles, diazocines, or hemithioindigo matched to your LEDs/filters.

How many Azo units do I need?

One internal Azo can shift Tm; 2–3 spaced units amplify the effect. Exact shift depends on placement and sequence context.

Will switching affect fluorescence readouts?

Switching changes absorption/stacking and can alter FRET/quencher behavior. We can co‑design dye/quencher placement for robust signals.

Speak to a Scientist

Typical response: <1 business day

References

  1. Reviews on azobenzene and visible‑light photoswitches for biomacromolecules.
  2. Photoregulated nucleic acid design principles and applications.
  3. Diarylethene switch fatigue resistance and bistability in bio‑contexts.

On request, we’ll align literature‑style switching conditions and placements to your instrument.

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.